Manufacturing new electrolytes with high ionic conductivity has been a crucial challenge in the development and large-scale distribution of fuel cell devices. In this work, we present two Nafion composite membranes containing a non-stoichiometric calcium titanate perovskite (CaTiO3−δ) as a filler. These membranes are proposed as a proton exchange electrolyte for Polymer Electrolyte Membrane (PEM) fuel cell devices. More precisely, two different perovskite concentrations of 5 wt% and 10 wt%, with respect to Nafion, are considered. The structural, morphological, and chemical properties of the composite membranes are studied, revealing an inhomogeneous distribution of the filler within the polymer matrix. Direct methanol fuel cell (DMFC) tests, at 110 °C and 2 M methanol concentration, were also performed. It was observed that the membrane containing 5 wt% of the additive allows the highest cell performance in comparison to the other samples, with a maximum power density of about 70 mW cm−2 at 200 mA cm−2. Consequently, the ability of the perovskite structure to support proton carriers is here confirmed, suggesting an interesting strategy to obtain successful materials for electrochemical devices.